Independent component analysis uncovers the landscape of the bladder tumor transcriptome and reveals insights into luminal and basal subtypes

Extracting relevant information from large-scale data offers unprecedented opportunities in cancerology. We applied independent component analysis (ICA) to bladder cancer transcriptome data sets and interpreted the components using gene enrichment analysis and tumor-associated molecular, clinicopath...

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Detalles Bibliográficos
Autores: Biton, Anne, Bernard-Pierrot, Isabelle, Lou, Yinjun, Krucker, Clémentine, Chapeaublanc, Elodie, Rubio Pérez, Carlota, 1990-, López Bigas, Núria, Kamoun, Aurélie, Neuzillet, Yann, Gestraud, Pierre, Grieco, Luca, Rebouissou, Sandra, deReyniès, Aurélien, Benhamou, Simone, Lebret, Thierry, Southgate, Jennifer, Barillot, Emmanuel, Allory, Yves, Zinovyev, Andrei, Radvanyi, François
Tipo de recurso: artículo
Estado:Versión aceptada para publicación
Fecha de publicación:2014
País:España
Institución:Universitat Pompeu Fabra
Repositorio:Repositorio Digital de la UPF
OAI Identifier:oai:repositori.upf.edu:10230/23723
Acceso en línea:http://hdl.handle.net/10230/23723
http://dx.doi.org/10.1016/j.celrep.2014.10.035
Access Level:acceso abierto
Palabra clave:Càncer -- Aspectes genètics -- Informàtica
Càncer -- Aspectes moleculars -- Informàtica
Descripción
Sumario:Extracting relevant information from large-scale data offers unprecedented opportunities in cancerology. We applied independent component analysis (ICA) to bladder cancer transcriptome data sets and interpreted the components using gene enrichment analysis and tumor-associated molecular, clinicopathological, and processing information. We identified components associated with biological processes of tumor cells or the tumor microenvironment, and other components revealed technical biases. Applying ICA to nine cancer types identified cancer-shared and bladder-cancer-specific components. We characterized the luminal and basal-like subtypes of muscle-invasive bladder cancers according to the components identified. The study of the urothelial differentiation component, specific to the luminal subtypes, showed that a molecular urothelial differentiation program was maintained even in those luminal tumors that had lost morphological differentiation. Study of the genomic alterations associated with this component coupled with functional studies revealed a protumorigenic role for PPARG in luminal tumors. Our results support the inclusion of ICA in the exploitation of multiscale data sets.

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